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Bioresources and Bioprocessing May 2022Prokaryotic Argonaute (pAgo) proteins are well-known oligonucleotide-directed endonucleases, which contain a conserved PIWI domain required for endonuclease activity....
BACKGROUND
Prokaryotic Argonaute (pAgo) proteins are well-known oligonucleotide-directed endonucleases, which contain a conserved PIWI domain required for endonuclease activity. Distantly related to pAgos, PIWI-RE family, which is defined as PIWI with conserved R and E residues, has been suggested to exhibit divergent activities. The distinctive biochemical properties and physiological functions of PIWI-RE family members need to be elucidated to explore their applications in gene editing.
RESULTS
Here, we describe the catalytic performance and cellular functions of a PIWI-RE family protein from Pseudomonas stutzeri (PsPIWI-RE). Structural modelling suggests that the protein possesses a PIWI structure similar to that of pAgo, but with different PAZ-like and N-terminal domains. Unlike previously reported pAgos, recombinant PsPIWI-RE acts as an RNA-guided DNA nuclease, as well as a DNA-guided RNA nuclease. It cleaves single-stranded DNA at temperatures ranging from 20 to 65 °C, with an optimum temperature of 45 °C. Mutation at D525 or D610 significantly reduced its endonuclease activity, confirming that both residues are key for catalysis. Comparing with wild-type, mutant with PIWI-RE knockout is more sensitive to ciprofloxacin as DNA replication inhibitor, suggesting PIWI-RE may potentially be involved in DNA replication.
CONCLUSION
Our study provides the first insights into the programmable nuclease activity and biological function of the unknown PIWI-RE family of proteins, emphasizing their important role in vivo and potential application in genomic DNA modification.
PubMed: 38647609
DOI: 10.1186/s40643-022-00539-x -
PloS One 2020High concentrations of metals in the environment alter bacterial diversity, selecting resistant and tolerant species. The study evaluated the selection of a potential...
High concentrations of metals in the environment alter bacterial diversity, selecting resistant and tolerant species. The study evaluated the selection of a potential bacterial strain from Sepetiba Bay-Rio de Janeiro, Brazil marine sediments to remove Cu and Pb. The bacterial strain isolated from the sediments was used in three different bioassays: (1) Cu at concentrations of 0 (control), 6 and 50 μg.mL-1; (2) Pb at concentrations of 0 (control), 6 and 50 μg.mL-1; (3) Cu + Pb in concentrations of 3 μg.mL-1 Cu + 3 μg.mL-1 Pb (6 μg.mL-1) and 25 μg.mL-1 Cu + 25 μg.mL-1 Pb (50 μg.mL-1). The number of cells and the enzymatic activities of dehydrogenases and esterases were quantified. Results of taxonomic identification indicated the selection of the Pseudomonas stutzeri W228 strain, showing a greater degree of similarity (±73%) with the database used. There was no significant variation in the number of cells, 108 cells.mL-1, which represents a high biomass production in the presence of stressors. However, we observed a reduction in dehydrogenase activity at all tested concentrations of Cu, Pb and Cu + Pb. The activity of esterase increased, indicating a higher energy demand to complete the bacterial life cycle. The study showed significant results for the absorption of Pb by the extracellular polymeric substances (EPS) and the efflux of Cu. The capacity of Pb absorption by EPS can be considered a resistance mechanism, as well as the efflux of Cu, so that the available EPS sites could be occupied by the most toxic ions demonstrating that Pseudomonas stutzeri is resistant to Pb and Cu.
Topics: Bacterial Proteins; Bacteriological Techniques; Biodegradation, Environmental; Biomass; Brazil; Copper; Esterases; Extracellular Polymeric Substance Matrix; Gene Expression Regulation, Bacterial; Gene Expression Regulation, Enzymologic; Geologic Sediments; Lead; Oxidoreductases; Pseudomonas stutzeri; Water Pollutants, Chemical
PubMed: 33104697
DOI: 10.1371/journal.pone.0240486 -
International Journal of Nanomedicine 2020Selenium nanoparticles (SeNP) have several applications in the field of biotechnology, including their use as anti-cancer drugs. The purpose of the present study is to...
PURPOSE
Selenium nanoparticles (SeNP) have several applications in the field of biotechnology, including their use as anti-cancer drugs. The purpose of the present study is to analyze the efficacy of green synthesis on the preparation of SeNP and its effect on their anti-cancer properties.
METHODS
A bacterial strain isolated from a freshwater source was shown to efficiently synthesize SeNP with potential therapeutic properties. The quality and stability of the NP were studied by scanning electron microscopy, X-ray diffraction, zeta-potential and FTIR analysis. A cost-effective medium formulation from biowaste having 6% banana peel extract enriched with 0.25 mM tryptophan was used to synthesize the NP. The NP after optimization was used to analyze their anti-tumor and anti-angiogenic activity. For this purpose, first, the cytotoxicity of the NP against cancer cells was analyzed by MTT assay and then chorioallantoic membrane assay was performed to assess anti-angiogenic activity. Further, cell migration assay and clonogenic inhibition assay were performed to test the anti-tumor properties of SeNP. To assess the cytotoxicity of SeNP on healthy RBC, hemolysis assay was performed.
RESULTS
The strain identified as (MH191156) produced phenazine carboxylic acid, which aids the conversion of Se oxyanions to reduced NP state, resulting in particles in the size range of 75 nm to 200 nm with improved stability and quality of SeNP, as observed by zeta (ξ) potential of the particles which was found to be -46.2 mV. Cytotoxicity of the SeNP was observed even at low concentrations such as 5 µg/mL against cervical cancer cell line, ie, HeLa cells. Further, neovascularization was inhibited by upto 30 % in CAMs of eggs coinoculated with SeNp when compared with untreated controls, indicating significant anti-angiogenic activity of SeNP. The NP also inhibited the invasiveness of HeLa cells as observed by decreased cell migration and clonogenic proliferation. These observations indicate significant anti-tumor and anti-angiogenic activity of the SeNP in cervical cancer cells.
CONCLUSION
(MH191156) is an efficient source of Se NP production with potential anti-angiogenic and anti-tumor properties, particularly against cervical cancer cells.
Topics: Angiogenesis Inhibitors; Animals; Antineoplastic Agents; Cell Death; Cell Movement; Cell Proliferation; Cell Survival; Chick Embryo; Costs and Cost Analysis; Female; HeLa Cells; Hemolysis; Humans; Metal Nanoparticles; Phenazines; Pseudomonas stutzeri; Reproducibility of Results; Selenium; Spectroscopy, Fourier Transform Infrared; Static Electricity; Uterine Cervical Neoplasms; X-Ray Diffraction
PubMed: 32606692
DOI: 10.2147/IJN.S247426 -
Scientific Reports Feb 2021The bacterium Pseudomonas stutzeri SPM-1, obtained from textile wastewater dumping sites of Surat, Gujarat was studied for the degradation of the textile azo dye Procion...
The bacterium Pseudomonas stutzeri SPM-1, obtained from textile wastewater dumping sites of Surat, Gujarat was studied for the degradation of the textile azo dye Procion Red-H3B. The optimization was carried on the phenanthrene enrichment medium followed by exposing it to variable environmental factors and nutritional sources. The complete decolorization of dye (50 mg/L) happened within 20 h of incubation at pH 8 and temperature 32 ± 0.2 °C under microaerophilic conditions. Decolourization was monitored with the shifting of absorbance peak in UV-Vis spectrophotometry and HPLC analysis. The physicochemical studies of effluent before and after the treatment revealed 85%, 90%, and 65% decline in BOD, COD, and TOC levels. The strain showed significant activities of azoreductase (95%), laccase (76%), and NADH-DCIP reductase (88%) at 12 h, 10 h, and 8 h of growth respectively indicating evidence for reductive cleavage of the dye. The changes in the functional groups were confirmed by the presence of new peaks in FT-IR data. GC-MS analysis helped in recognizing the degraded dye compounds thus elucidating the proposed pathway for degradation of Procion Red-H3B. The potential of the bioremediation process was concluded by a phytotoxicity test using two plants, Vigna radiata and Cicer arietinum. Our study demonstrates that the strain Pseudomonas stutzeri SPM-1 has rapid decolorization efficiency and holds a noteworthy perspective in industrial application for textile wastewater treatment.
Topics: Azo Compounds; Biodegradation, Environmental; Gas Chromatography-Mass Spectrometry; Humans; Pseudomonas stutzeri; Spectroscopy, Fourier Transform Infrared; Triazines; Wastewater; Water Pollutants, Chemical; Water Purification
PubMed: 33542307
DOI: 10.1038/s41598-021-82494-9 -
Journal of Infection and Public Health 2019We report a case of Pseudomonas stutzeri endocarditis in Lebanon. The patient had a recent history of prosthetic aortic valve replacement and presented to the emergency... (Review)
Review
We report a case of Pseudomonas stutzeri endocarditis in Lebanon. The patient had a recent history of prosthetic aortic valve replacement and presented to the emergency department with fever and chills. Transesophageal echocardiography confirmed the presence of a vegetation on the prosthetic valve and blood cultures yielded P. stutzeri. The patient was treated with surgery and antibiotics but deteriorated and passed away four days after admission. To our knowledge, this is the fifth case of P. stutzeri endocarditis reported in the literature, and the first case with early presentation and mortality.
Topics: Aged; Anti-Bacterial Agents; Aortic Valve; Ceftazidime; Chills; Diagnosis, Differential; Echocardiography, Transesophageal; Endocarditis, Bacterial; Heart Valve Prosthesis; Heart Valve Prosthesis Implantation; Humans; Infusions, Intravenous; Male; Postoperative Complications; Prosthesis-Related Infections; Pseudomonas stutzeri
PubMed: 30049610
DOI: 10.1016/j.jiph.2018.07.004 -
Applied and Environmental Microbiology Feb 2021Diazotrophs can produce bioavailable nitrogen from inert N gas by bioelectrochemical nitrogen fixation (-BNF), which is emerging as an energy-saving and highly selective...
Diazotrophs can produce bioavailable nitrogen from inert N gas by bioelectrochemical nitrogen fixation (-BNF), which is emerging as an energy-saving and highly selective strategy for agriculture and industry. However, current -BNF technology is impeded by requirements for NH assimilation inhibitors to facilitate intracellular ammonia secretion and precious metal catalysts to generate H as the energy-carrying intermediate. Here, we initially demonstrate inhibitor- and catalystless extracellular NH production by the diazotroph Pseudomonas stutzeri A1501 using an electrode as the sole electron donor. Multiple lines of evidence revealed that P. stutzeri produced 2.32 ± 0.25 mg/liter extracellular NH at a poised potential of -0.3 V (versus standard hydrogen electrode [SHE]) without the addition of inhibitors or expensive catalysts. The electron uptake mechanism was attributed to the endogenous electron shuttle phenazine-1-carboxylic acid, which was excreted by P. stutzeri and mediated electron transfer from electrodes into cells to directly drive N fixation. The faradaic efficiency was 20% ± 3%, which was 2 to 4 times that of previous -BNF attempts using the H-mediated pathway. This study reports a diazotroph capable of producing secretable NH via extracellular electron uptake, which has important implications for optimizing the performance of -BNF systems and exploring the novel nitrogen-fixing mode of syntrophic microbial communities in the natural environment. Ammonia greatly affects global ecology, agriculture, and the food industry. Diazotrophs with an enhanced capacity of extracellular NH excretion have been proven to be more beneficial to the growth of microalgae and plants, whereas most previously reported diazotrophs produce intracellular organic nitrogen in the absence of chemical suppression and genetic manipulation. Here, we demonstrate that Pseudomonas stutzeri A1501 is capable of extracellular NH production without chemical suppression or genetic manipulation when the extracellular electrode is used as the sole electron donor. We also reveal the electron uptake pathway from the extracellular electron-donating partner to P. stutzeri A1501 via redox electron shuttle phenazines. Since both P. stutzeri A1501 and potential electron-donating partners (such as electroactive microbes and natural semiconductor minerals) are abundant in diverse soils and sediments, P. stutzeri A1501 has broader implications on the improvement of nitrogen fertilization in the natural environment.
Topics: Ammonia; Nitrogen Fixation; Pseudomonas stutzeri
PubMed: 33310714
DOI: 10.1128/AEM.01998-20 -
Frontiers in Bioscience (Landmark... Jan 2023wilt and blight are the most important diseases of chickpea. The current study was designed to investigate the individual and combined effect of salicylic acid (SA)...
BACKGROUND
wilt and blight are the most important diseases of chickpea. The current study was designed to investigate the individual and combined effect of salicylic acid (SA) with and to suppress wilt and promote growth of chickpea varieties: Thal-2006 and Punjab-2008.
METHODS
At the time of sowing, inoculum of was applied to the soil and the incidence of wilt was recorded after 60 days. The seeds were inoculated with and prior to sowing. Chickpea plants were treated with salicylic acid at seedling stage.
RESULTS
The combination of and SA significantly increased root length (166% and 145%), shoot height (50% and 47%) and shoot biomass (300% and 233%) in cv. Thal-2006 and cv. Punjab-2008, respectively, in infected plants. Similarly, the combined treatment of + SA, also enhanced the plant growth parameters of chickpea varieties. Maximum reduction in disease severity was observed in both + SA (90% and 84%) and + SA (79% and 77%) treatments in cv. Thal-2006 and Punjab-2008, respectively. Both + SA and + SA treatments resulted in increased leaf relative water and total protein content, peroxidase, superoxide dismutase, phenylalanine ammonia-lyase and polyphenol oxidase activities in both resistant (cv. Thal-2006) and susceptible (cv. Punjab-2008) cultivars. Both treatments also significantly reduced malondialdehyde (MDA) and proline content in cv. Thal-2006 and Punjab-2008. Cultivar Thal-2006 was more effective than cv. Punjab-2008.
CONCLUSIONS
The results suggested that, in combination, salicylic acid and may play an important role in controlling wilt diseases by inducing systemic resistance in chickpea.
Topics: Biomass; Cicer; Combined Modality Therapy; Fusarium; Malondialdehyde; Plant Diseases; Salicylic Acid; Pseudomonas; Agricultural Inoculants
PubMed: 36722276
DOI: 10.31083/j.fbl2801020 -
Analytical Chemistry Aug 2023Small proteins of around 50 aa in length have been largely overlooked in genetic and biochemical assays due to the inherent challenges with detecting and characterizing...
Small proteins of around 50 aa in length have been largely overlooked in genetic and biochemical assays due to the inherent challenges with detecting and characterizing them. Recent discoveries of their critical roles in many biological processes have led to an increased recognition of the importance of small proteins for basic research and as potential new drug targets. One example is CcoM, a 36 aa subunit of the -type oxidase that plays an essential role in adaptation to oxygen-limited conditions in , a model for the clinically relevant, opportunistic pathogen . However, as no comprehensive data were available in , we devised an integrated, generic approach to study small proteins more systematically. Using the first complete genome as basis, we conducted bottom-up proteomics analyses and established a digest-free, direct-sequencing proteomics approach to study cells grown under aerobic and oxygen-limiting conditions. Finally, we also applied a proteogenomics pipeline to identify missed protein-coding genes. Overall, we identified 2921 known and 29 novel proteins, many of which were differentially regulated. Among 176 small proteins 16 were novel. Direct sequencing, featuring a specialized precursor acquisition scheme, exhibited advantages in the detection of small proteins with higher (up to 100%) sequence coverage and more spectral counts, including sequences with high proline content. Three novel small proteins, uniquely identified by direct sequencing and not conserved beyond , were predicted to form an operon with a conserved protein and may represent genes. These data demonstrate the power of this combined approach to study small proteins in and show its potential for other prokaryotes.
Topics: Pseudomonas stutzeri; Proteomics; Proteogenomics; Pseudomonas aeruginosa; Oxygen
PubMed: 37535005
DOI: 10.1021/acs.analchem.3c00676 -
Infection and Drug Resistance 2021To investigate the genomic and plasmid characteristics of a newly discovered strain with a -carrying plasmid and novel integron In isolated from a cerebrospinal fluid...
PURPOSE
To investigate the genomic and plasmid characteristics of a newly discovered strain with a -carrying plasmid and novel integron In isolated from a cerebrospinal fluid specimen in a teaching hospital.
METHODS
Species identification was performed by MALDI-TOF MS, and was identified by PCR and Sanger sequencing. Whole-genome sequencing analysis was conducted using the Illumina NovaSeq 6000 and Oxford Nanopore platforms. Integron detection was performed using INTEGRALL. The phylogenetic tree was constructed by using kSNP3.0. Plasmid characteristics were assessed by S1-pulsed-field gel electrophoresis (S1-PFGE), Southern blotting, conjugation experiments, and whole-genome sequencing analysis. Comparative genomics analysis of the plasmid and genetic context of were conducted by using BLAST Ring Image Generator (BRIG) and Easyfig 2.3, respectively.
RESULTS
ZDHY95, an MDR strain of harboring , was identified. It was sensitive only to amikacin and was resistant to carbapenems, β-lactams, aztreonam, fluoroquinolones, and aminoglycosides. Joint S1-PFGE, Southern blot, conjugation assay, and whole-genome sequencing experiments confirmed that the gene was located within class I integron In of the plasmid and that the surrounding genetic environment was 5'CS- --3'CS. The novel class I integron In was detected on the chromosome of ZDHY95, and the gene cassette array was 5'CS- --3'CS. Phylogenetic analysis showed that antimicrobial resistance gene-carrying isolates were divided into two clusters, mainly containing isolates from the USA and Pakistan.
CONCLUSION
A novel -carrying conjugative plasmid, pZDHY95-VIM-2, was reported for the first time in , elucidating the genetic environment and transfer mechanism. The gene structure of the novel class I integron In was also clarified. We explored the phylogenetic relationship of with drug resistance genes and suggested that with metallo-β-lactamases (MBLs) in the hospital environment may cause infection in patients with long-term intubation or after interventional surgery.
PubMed: 34466007
DOI: 10.2147/IDR.S320294 -
Case Reports in Ophthalmology 2020A patient presented with complaints of a sudden decrease in vision, ocular redness, and pain in the right eye. The patient had a history of clear lens extraction with...
A patient presented with complaints of a sudden decrease in vision, ocular redness, and pain in the right eye. The patient had a history of clear lens extraction with intraocular lens (IOL) implantation for myopia 2 years previously. He had been prescribed topical steroids for episodes of inflammation that occurred repeatedly every 1-2 months. With a presumptive diagnosis of chronic endophthalmitis, a 23-G transconjunctival sutureless pars plana vitrectomy (PPV) with delivery of intravitreal antibiotics was performed the next day. Culture sensitivity testing of the vitreous sample indicated that was sensitive to ceftazidime and gentamicin. Two weeks later, the patient presented with sudden loss of vision and all the signs of recurrent endophthalmitis. 23-G transconjunctival sutureless PPV was performed along with removal of the posterior chamber IOL through a corneal incision. Complete resolution was only achieved after removal of the IOL, resulting in excellent visual recovery. Due to its chronic and fulminating nature, can induce endophthalmitis and should be considered in the differential diagnosis. Aseptic measures are the best prevention.
PubMed: 33437233
DOI: 10.1159/000510129